If you define all laws of reality as physics, then sure, there's nothing physics can't explain. But that's, well . . . here, let me tell a fable to explain.
The year 152,036 AD
"Hey, we just got the third-check output from the LMC computer array."
"Yeah? What did it say?"
"The previous two sets were right. We input the known masses of the fundamental particles to five hundred thousand digits, and the known strengths of all seven fundamental forces to the same, arrange them in the form of a vertebrate animal, and run the sim, we do get an almost-perfect simulation. Minus the Lacuna. In fact, we can now say the evidence for the Lacuna has hit fifty-three sigma."
"Damn. Any good news on the eighth force candidates?"
"All of them still cause the Sun to fail to fuse, if we allow them to have any measurable effect on covalently-bonded masses smaller than 0.997312121 milligrams."
"And the collider results completely rule out any of the gauge bosons that fit any of the fifteen proposed models of an eighth force compatible with no effect under a milligram of mass. In fact, they don't show any evidence of any gauge bosons associated with an eighth force, anywhere short of ten quadrillion yottavolts."
"They've said that for the last hundred thousand years, why would you expect a change now?"
"Look, this is nuts. There is no way that physics has a special force just to explain the Lacuna, and has no affect on anything else, and no other way to detect it than the existence of the Lacuna."
"Fifty-three sigma. The universe doesn't care about your incredulity."
"Yeah, but it's stupid. How the hell did we wind up in a universe that requires a special law of physics to explain the Lacuna?"
"Because the Creators chose to add it when they were creating the Universe Simulation."
"Dammit. I still don't believe it. What kind of genius develops a perfectly good set of fundamental laws, implicit in a single equation you can fit on a T-shirt, that creates all the beauty and wonder of the universe, and then sticks on a pointless extraneous natural law to do absolutely nothing but make a handful of vertebrates, of all things, yawn?"
"You have met software engineers, haven't you?"
"I'm going to go get drunk."
I don't understand your point. If there is a separate law required for yawns then that's still a physical law that describes physical systems.
Concretizing the abstract is an interesting blog post in that it makes a relatively cogent argument for non-reductionism. While I don't agree with it, I found it useful in that it helped me better understand how intelligent non-reductionists think. It also helped clarify to me an old distinction, that of philosophers versus engineers.
I find this interesting in the way that smart people are likely to disagree with the correct interpretation of some of its claims - while others would say the post is worshipping the mysterious, others would say that it's just making reasonable cautions about the inherent methodological limitations of a certain approach. One might even think that it's essentially making a similar point as Eliezer's warning about floating beliefs, and therefore to agree with the Sequences. The caution of "beware of thinking that your abstractions say everything that there is to be said about something" is a reasonable one, and people do clearly make that mistake sometimes.
I expect that part of what influences how plausible one finds this argument depends on whether one has more of an "engineer's mindset" or a "philosopher's mindset". Somebody with an engineer's mindset will think that "yes, the abstractions we use might be imperfect, but what else do you propose we use? They're still the best tool for accomplishing stuff, and anything else is just philosophcial nonsense that isn't grounded in anything". Whereas the philosopher is less interested in using their knowledge to "accomplish stuff", and more interested in the ideas and their implications themselves.
As an aside, this distinction might be part of the reason why we have so many computer or hard science folks on this site. Partially it's because Eliezer used a lot of CS jargon in writing the Sequences, but probably also because the Sequences, while philosophical in nature, are also very focused on practical results and getting empirical predictions out of your beliefs.
Looking at what we could use this distinction for (and thus taking an engineer's mindset) some people here have mentioned getting an "ick" reaction from religious people, just due to those people having strong false beliefs. I think that, combined with properly understanding the emotional basis of religion, an understanding of the philosopher / engineer distinction can help avoid that reaction. Our values determine our beliefs, and there are plenty of religious people who aren't stupid, crazy, or anything like that. They might simply be philosophers instead of engineers, or they might be engineers who are more interested in the instrumental benefits of religion than the rather marginal benefits of x-rationality. (Amusingly, such a "religious engineer" might justifiably consider our obsession with "truth" as just an odd philosophical pursuit.)